When Hopper escapes from the pet shop and makes friends with Zucker, the crown prince of Atlantia, he is faced with helping them solve an enormous injustice within their government's diplomatic relations, and Hopper must struggle to discover qualities he didn't know he had. Zucker, crown rat prince of Atlantia, located below New York's subways, curiously sneaks outside the city walls one day only to be saved (from one of their own cat guards) by a courageous mouse named Dodger. From Dodger, Zucker discovers a secret: his father Titus the emperor has created and maintained his peace accord with the cats only by ensuring them regular meals of fat rats, mice, and squirrels from Atlantia's refugee camps. Unsuspecting refugees, supposed beneficiaries of Titus' “kind” policies, are sent to “colonize” outside the city walls, only to be trapped and eaten by the cats, who then serve as friendly guards for the safe rat citizens of Atlantia. Dodger belongs to the Mus, a mouse tribe which has discovered this fact, and is in the process of forming an alliance with rats who also know the secret, led by a ferocious female rat named Firren. At first, Zucker doesn't believe it. When he returns to the castle, his father has sent his own wife (Zucker's mother) to lead a group of “colonists” to their deaths. Titus and the cat queen Felina don't admit the gruesome details outright, but with his new intelligence from Dodger and Firren, he is able to read between the lines. That is the beginning of Zucker's life as a double agent. This the reader learns through the prologue and epilogue.
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Through flashbacks, the reader learns that Dodger then disappears. Most of the story is told through the eyes of Hopper, Dodger's son, who grows up with his mother, sister, and brother in a New York pet shop. When they escape, they are separated. Dodger finds his way to Atlantia; his sister Pinkie, to the Mus; and his brother, to Atlantia's refugee camp.
Hopper quickly makes friends with Zucker, but Zucker is not able to openly tell him the truth about his father's alliance with his father's guards around. Hopper is quickly labeled as “special.” Everyone recognizes him as Dodger's son and a prophecied Mus hero because of a ring around one eye that he inherited from his father. Hopper doesn't even remember Dodger and doesn't know why it's important, though he picks up some clues along the way. Though Zucker can't tell him much, he does teach Hopper to read.
While visiting the refugee camp with Zucker, Hopper is “kidnapped” by a friendly but watchful Firren, who takes him back to the Mus to present him as the “Chosen One.” With the Mus, they discover that Pinkie, who has a white ring around her other eye, has been set up as the “Chosen One.” She is a vengeful, easily angered mouse, and is annoyed when they decide to replace her with Hopper. The goal is to attack Atlantia, free the “refugees,” and overthrow Titus. Hopper accepts, but only to act as a double agent and help Titus, who he still believes to be good. Using the Mus' subway map and his newfound reading skills, he also figures out how to navigate using subway trains.
Firren and Zucker encounter each other and fight because Firren thinks Zucker has betrayed him due to Hopper's misinterpretation of Zucker's words in Atlantia. Zucker is wounded, and Hopper goes back with him, while Pinkie stays with Firren and the Mus. Hopper takes the subway to get help for Zucker, and while in Atlantia, tells Titus of the upcoming attack by the Mus. Firren has given him valuable advice about trusting his instincts, however, and Hopper stops when he realizes something is wrong. This is confirmed when a maid leads him to overhear a conversation between Titus and Queen Felina.
When Zucker returns to Atlantia in disguise, Zucker explains himself and his false words to fool the guards, and apologizes. Hopper understands the situation now and regrets having told Titus even as much as he did. They must make the best of it however. They and several allies collect weapons to distribute to the refugees, and tell them of the danger. Some believe them, but not all. Zucker, however, is captured, and Hopper and his little brother are swept away in a rush “colonization” effort requested by Felina, who doesn't trust Titus' continuing ability to fulfill his end of the bargain, especially if Firren's raid succeeds.
Zucker has sent messages to Firren and the Mus, however. Firren brings reinforcements to help the “colonists,” and they defeat the cats that have come to eat them. She sends Mus to free the refugees, where many refugees (who have realized the truth of Hopper's warning) join the effort. The citizens of Atlantia begin to flee, no longer guaranteed safety from the cats. Titus is trapped by grasshoppers, sent by Firren, in his castle; only Zucker is allowed in to talk with him. Hopper ultimately stays with Zucker and intends to help rebuild a better Atlantia. Pinkie returns to the Mus, where she is once again (since Hopper's return to Zucker) recognized as the Chosen One. Their little brother, afraid to remain in Atlantia, goes with Pinkie to live with the Mus, to Hopper's dismay. But there is hope: an idolized figure called “La Rocha,” treated as a god by the Mus, has communicated with the Mus since the beginning, and sends Hopper a message that he will be with him soon. Hints within the book suggest it may be his father, Dodger.
Best part of story, including ending:
Zucker is very down-to-earth in his interactions with Hopper. He feels he has been betrayed as much as the refugees have been, and is therefore committed to helping them (though of course he doesn't tell his father that).
Best scene in story:
When Hopper returns to Atlantia and tells Titus about Firren's upcoming raid, Titus' response immediately sits wrong with Hopper. Though he is inexperienced and has been told to distrust Firren, he takes a very good piece of her advice: to trust his gut. He shuts his mouth and is very glad to have done so shortly afterwards.
Opinion about the main character:
Hopper has a good heart and cares about his siblings and friends. He is also pretty smart, learning to read in a matter of weeks and deciphering a subway map no other mouse or rat has deciphered. He is, however, inexperienced and naive.